Intro to Chemistry: Reactions & Interactions

In this post, I’m only going to cover information that is relevant to people studying Anatomy & Physiology or Biology. Personally, I’m in a long-term love-hate relationship with Chemistry.

So, last time we discussed the atom. Why? Because atoms make up molecules and molecules are where it gets interesting. But what are molecules and how do we make them? Let’s address some terminology first:

  • Compound — made up of 2 (or more) elements
  • Molecule — made up of 2 (or more) atoms

A compound is any 2 (or more) elements, bonded together. A molecule is any 2 (or more) atoms bonded together. They sound very similar. It’s one of those “a square is a rectangle, but a rectangle is not a square” kind of things.

Basically, in a compound, the 2+ atoms have to be of different elements, but that’s not the case with molecules, which can be made of any element or elements. For example:

  • O2 (also known as “molecular oxygen”) is a molecule because it has 2 or more atoms
  • H2O (also known as “water”) is a compound because it has 2 or more elements (H and O)
    • It is also a molecule because it has 2 or more atoms

Textbooks always emphasize the difference between compounds and molecules. Maybe the distinction is significant to chemists, but guess what? It never comes up again in Physiology because all compounds, by definition, are molecules. We will only ever use the term molecule.

Covalent Bonds

So how do we bring together Hydrogen and Oxygen, to make a molecule of water? Atoms have to be bonded to one another with… bonds. There are a number of different types of bonds, but the most important is called a covalent bond.

Remember that in an atom, we have a nucleus at the center, which contains protons and neutrons. Orbiting the nucleus, we have electrons. Those electrons are found in layers called shells. The first shell, which is the one closest to the nucleus, can hold up to 2 electrons. If an element has more than 2 electrons, we start filling up the next shell. This shell can hold up to 8 electrons. Some elements can be massive with over 100 electrons and several shells. But in Physiology and Biology, we mainly work with Hydrogen, Carbon, Nitrogen, and Oxygen — all of which are pretty small.

The outermost shell of an atom, whichever shell that may be, is called the valence shell. This shell is where covalent bonds will be formed. From the name, you might guess that these bonds involve sharing electrons in the valence shell.

The octet rule tells us that atoms will attempt to either fill or empty their valence shell. So, let’s take an example:

Hydrogen has 1 electron. It’s valence shell can hold 2 electrons. To fill the valence shell, how many electrons does Hydrogen need to pick up? Yeah, 1. You got it.

Oxygen has 8 electrons. 2 go in the first electron shell. How many are left over? You got it — 6 electrons. If Oxygen has 6 electrons in its outermost shell, its valence shell, how many does it need to fill the valence shell? Remember, the second electron shell can hold 8 electrons, so Oxygen needs to pick up 2 more electrons.

And so, Oxygen and Hydrogen come together to form water. H2O is made when two hydrogens and one oxygen form covalent bonds. The two hydrogens each let the oxygen borrow their electrons (1 each) some of the time. This means that, some of the time, oxygen will have 8 electrons in its valence shell. And oxygen shares an electron with each of the hydrogens (some of the time) so they will have 2 electrons in their valence shells. This arrangement is energetically stable, so covalent bonds are usually pretty strong.

Ionic Bonds and Polarity

Atoms and molecules can be neutral or they can be electrically charged (positively or negatively charged). Typically, atoms are neutral because the number of positive charges (protons) is equal to the number of negative charges (electrons). They balance each other out. If an atom loses an electron, it becomes positively charged because it lost a negative charge.

When atoms or molecules, which have opposite charges, come together, this is called an ionic bond. They are bonded by their charge. You’ve heard that opposites attract, right? Positively and negatively charged atoms are attracted to each other, as well.

For example, take Sodium Chloride (NaCl). In this ionic compound, positively charged sodium (Na+) is attracted to negatively charged chloride (Cl-).

Sometimes a molecule will have a partial charge in one region and a different charge in another region. The molecule has different charges at different ends, so we call these ends poles and this phenomenon polarity. It may be helpful to consider another example:

In H2O, Oxygen is bigger than Hydrogen. It’s about 16 times heavier, too. It’s a bully, who made an arrangement to share electrons with the hydrogens, but it holds onto them longer than it should. In science words, we would say it is more electronegative than hydrogen. As a result, the end of the molecule where we find oxygen is going to have a partial negative charge. The end where we find the hydrogens will have a slight positive charge.

Water is polar and this polarity is one of the most important characteristics of water. This polarity causes water molecules to stick to one another — the slightly positive end of one water molecule is attracted to the slightly negative end of another water molecule. It also allows charged molecules, such as salt and sugar, to dissolve in water. Lastly, it means that electrically neutral molecules, such as the lipids that make up the cell’s membrane, cannot dissolve in water.

Let’s pick it up with the cell membrane in the next post!

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